ArticleJournal of chemical theory and computation2013
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration.RSC advances · 2022Article
- Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels.Frontiers in physiology · 2021Review
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- Mechanistic Landscape of Membrane-Permeabilizing Peptides.Chemical reviews · 2019Review
- Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.Journal of chemical information and modeling · 2019Article
- A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.Biophysical journal · 2018Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Computational studies of peptide-induced membrane pore formation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.Journal of computational chemistry · 2017Article
- Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.Journal of chemical theory and computation · 2017Article
- New Continuum Approaches for Determining Protein-Induced Membrane Deformations.Biophysical journal · 2017Article
- Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models.Biochimica et biophysica acta · 2016Review
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.Biophysical journal · 2015Article
- Membrane environment modulates the pKa values of transmembrane helices.The journal of physical chemistry. B · 2015Article
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2 authors.
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Abstract
An extension to the heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is presented to allow dynamic membrane deformations in response to membrane-inserted biomolecules during molecular dynamic simulations. The flexible membrane is implemented through additional degrees of freedom that represent the membrane deformation at the contact points of a membrane-inserted solute with the membrane. The extra degrees of freedom determine the dielectric and non-polar solvation free energy profiles that are used to obtain the solvation free energy in the presence of the membrane and are used to calculate membrane deformation free energies according to an elastic membrane model. With the dynamic HDGB (DHDGB) model the membrane is able to deform in response to the insertion of charged molecules thereby avoiding the overestimation of insertion free energies with static membrane models. The DHDGB model also allows the membrane to respond to the insertion of membrane-spanning solutes with hydrophobic mismatch. The model is tested with the membrane insertion of amino acid side chain analogs, arginine-containing helices, the WALP23 peptide, and the gramicidin A channel.
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